ACS_ADS_DE_plot: DE evidence visualization with c-scores and d-scores
In CAMO-R/Rpackage: Perform cross-species resemblance analysis

ACS_ADS_DE_plot

R Documentation

DE evidence visualization with c-scores and d-scores

Description

The ACS_ADS_DE_plot is function to visualize DE evidence and the significance of c-scores and d-scores in one plot. X and y axes represent the average DE posterior probabilities in each study pair, size of dots represent the significance of c-scores (upper right) or d-scores (lower left).

Usage

ACS_ADS_DE_plot(
  mcmc.merge.list,
  ACS_ADS_pathway,
  dataset.names,
  cluster.lb = NULL,
  select.pathway.list,
  highlight.pathway.index = NULL,
  plot.path = NULL
)

Arguments

`mcmc.merge.list:`	a list of merged MCMC output matrices.
`ACS_ADS_pathway:`	a list of four data frames: pathway specific c-scores, d-scores and their permuted p-value (rows are pathways and columns are studies).
`dataset.names:`	a vector of dataset names.
`cluster.lb:`	a vector of cluster label named by pathway names. optional.
`select.pathway.list:`	a list of selected pathways (containing gene components).
`highlight.pathway.index:`	a numeric vector indicating which pathways in the select.pathway.list need to be highlighted.

Value

A collection of DE evidence plots for each data pair. In each individual panel, each dot is a pathway sized by p(c-score) (orange in upper right) or p(d-score) (blue in lower left).X and y axes are the average absolute DE posterior probabilities.

Examples

## Not run: 
#mcmc.merge.list from the merge step (see the example in function 'merge')
#select.pathway.list from the pathSelect step (see the example in function 'pathSelect')
#ACS_ADS_pathway from the multi_ACS_ADS_pathway step (see the example in 'multi_ACS_ADS_pathway')
#highlight and label the first three pathways in selec.pathway.list:
highlight.pathway.index = c(1,2,3)
ACS_ADS_DE_plot = function(mcmc.merge.list,ACS_ADS_pathway,dataset.names,
                           cluster.lb=NULL,select.pathway.list,
                           highlight.pathway.index=highlight.pathway.index,plot.path=NULL)

## End(Not run)

CAMO-R/Rpackage documentation built on July 20, 2023, 6:04 a.m.